Sodium in PDB 4afx: Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group

The structure of Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group, PDB code: 4afx was solved by A.Zhou, Y.Yan, Z.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.52 / 2.09
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.850, 106.660, 81.163, 90.00, 112.58, 90.00
R / Rfree (%)	21 / 24.9

The structure of Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group (pdb code 4afx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group, PDB code: 4afx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1387 b:45.8 occ:1.00 OE1 A:GLU292 2.9 52.7 1.0 CE1 B:HIS400 3.9 28.3 1.0 CD A:GLU292 3.9 50.2 1.0 N A:LEU291 4.0 52.3 1.0 NH1 B:ARG416 4.1 48.0 1.0 CA A:ALA290 4.1 56.6 1.0 OE2 A:GLU292 4.3 47.3 1.0 NE2 B:HIS400 4.4 29.6 1.0 C A:ALA290 4.5 54.5 1.0 CB A:ALA290 4.6 57.1 1.0 CD B:ARG416 4.6 37.3 1.0 N A:GLU292 4.9 47.1 1.0 O A:LEU289 4.9 60.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Reactive Loop Cleaved Zpi in I2 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1391 b:58.4 occ:1.00 NE2 A:GLN102 3.5 35.6 1.0 NH2 A:ARG338 3.7 42.5 1.0 NH1 A:ARG338 4.2 40.6 1.0 CG A:GLN102 4.2 35.6 1.0 CD A:GLN102 4.3 36.3 1.0 NH2 A:ARG337 4.4 43.4 1.0 CZ A:ARG338 4.4 41.8 1.0 CB A:GLN102 4.5 36.1 1.0

X.Huang, Y.Yan, Y.Tu, J.Gatti, G.J.J.Broze, A.Zhou, S.T.Olson. Structural Basis For Catalytic Activation of Protein Z-Dependent Protease Inhibitor (Zpi) By Protein Z. Blood V. 120 1726 2012.
ISSN: ISSN 0006-4971
PubMed: 22786881
DOI: 10.1182/BLOOD-2012-03-419598